Thermal niche summaries for Chinook Salmon

Spawning habitat will be summarized for July, August, and September, whereas rearing habitat is summarized for June, July, and August.

##Interannual Variability of all Chinook habitat To summarize interannual variability of Chinook habitat we averaged temperatures from June 1 - September 30 for each year and plotted the results. Stanadard deviation of yearly averages represent the spatial variability of RCAs.
Mean annual temperatures for Chinook habitat
year mean std
1980 7.99 2.19
1981 8.20 2.58
1982 7.75 2.11
1983 8.29 2.60
1984 8.95 2.32
1985 7.60 2.44
1986 7.75 2.16
1987 8.12 2.73
1988 8.32 2.34
1989 9.22 2.42
1990 8.86 2.39
1991 8.34 2.07
1992 7.41 3.36
1993 9.41 2.68
1994 8.46 2.62
1995 8.83 2.03
1996 7.96 2.74
1997 9.40 2.49
1998 7.90 2.29
1999 8.40 2.32
2000 7.81 2.46
2001 9.15 2.29
2002 8.71 2.35
2003 9.06 2.95
2004 9.58 3.54
2005 9.69 2.43
2006 8.39 2.02
2007 8.89 2.23
2008 7.72 2.21
2009 8.40 2.76
2010 8.18 2.16
2011 7.81 2.23
2012 7.74 2.26
2013 9.14 3.10
2014 8.58 2.50
2015 8.75 3.23
2016 9.74 2.63
2017 8.75 2.45
2018 9.06 2.22
##Interannual variability of monthly temperatures Average monthly temperatures were summ
Mean June temperatures for Chinook habitat
year month mean std
1980 6 7.67 1.97
1981 6 7.83 2.02
1982 6 6.83 1.84
1983 6 8.22 1.80
1984 6 8.63 1.83
1985 6 6.19 2.39
1986 6 7.30 2.30
1987 6 7.24 1.71
1988 6 8.13 1.72
1989 6 7.98 2.40
1990 6 9.00 2.11
1991 6 8.02 2.33
1992 6 7.99 2.09
1993 6 8.37 1.94
1994 6 8.25 2.19
1995 6 8.07 2.33
1996 6 7.79 2.30
1997 6 8.99 2.76
1998 6 7.80 2.01
1999 6 7.72 1.96
2000 6 7.43 2.20
2001 6 9.38 2.22
2002 6 7.98 2.19
2003 6 8.10 2.07
2004 6 9.74 2.36
2005 6 9.55 2.14
2006 6 7.82 1.63
2007 6 8.26 2.20
2008 6 6.85 1.91
2009 6 7.57 1.88
2010 6 7.42 1.83
2011 6 7.29 1.92
2012 6 7.78 2.36
2013 6 10.00 2.77
2014 6 7.56 2.04
2015 6 9.76 3.21
2016 6 9.51 2.05
2017 6 8.34 1.82
2018 6 8.01 1.80
Mean July temperatures for Chinook habitat
year month mean std
1980 7 9.62 1.82
1981 7 9.86 1.58
1982 7 9.03 1.88
1983 7 9.94 1.50
1984 7 9.95 1.56
1985 7 9.59 1.68
1986 7 9.25 1.76
1987 7 9.76 2.47
1988 7 9.96 1.65
1989 7 10.54 1.78
1990 7 9.93 1.68
1991 7 9.57 1.63
1992 7 9.73 1.82
1993 7 11.39 2.20
1994 7 9.56 1.81
1995 7 9.92 1.73
1996 7 9.75 1.64
1997 7 11.06 1.67
1998 7 9.65 1.64
1999 7 9.91 1.80
2000 7 9.19 2.00
2001 7 10.07 1.75
2002 7 10.27 1.74
2003 7 11.60 1.94
2004 7 11.76 2.27
2005 7 11.54 1.74
2006 7 9.91 1.62
2007 7 10.07 1.63
2008 7 8.76 1.82
2009 7 10.79 2.18
2010 7 8.97 1.69
2011 7 9.33 1.66
2012 7 8.50 1.83
2013 7 11.16 2.43
2014 7 10.35 1.78
2015 7 10.54 1.68
2016 7 11.69 1.87
2017 7 11.02 1.72
2018 7 10.58 2.20
Mean August temperatures for Chinook habitat
year month mean std
1980 8 8.35 1.60
1981 8 9.22 1.69
1982 8 8.91 1.34
1983 8 9.55 1.75
1984 8 10.31 2.46
1985 8 8.48 1.50
1986 8 8.06 1.51
1987 8 9.87 1.60
1988 8 9.39 1.50
1989 8 10.55 1.67
1990 8 10.02 1.80
1991 8 8.63 1.50
1992 8 8.55 2.18
1993 8 10.63 1.82
1994 8 9.98 2.25
1995 8 9.24 1.57
1996 8 9.07 1.49
1997 8 10.11 1.59
1998 8 8.00 2.22
1999 8 9.45 1.78
2000 8 8.94 1.93
2001 8 10.23 1.71
2002 8 9.62 1.83
2003 8 10.15 2.29
2004 8 11.60 1.97
2005 8 10.36 1.74
2006 8 8.87 1.66
2007 8 10.05 1.62
2008 8 8.93 1.58
2009 8 8.96 1.56
2010 8 9.21 1.69
2011 8 8.54 1.65
2012 8 8.73 1.53
2013 8 9.47 1.61
2014 8 9.65 1.89
2015 8 9.50 2.09
2016 8 10.61 1.52
2017 8 9.07 2.08
2018 8 9.75 1.90
Mean September temperatures for Chinook habitat
year month mean std
1980 9 6.24 1.89
1981 9 5.78 2.76
1982 9 6.14 1.63
1983 9 5.37 2.42
1984 9 6.84 1.53
1985 9 6.05 1.98
1986 9 6.31 1.83
1987 9 5.50 2.20
1988 9 5.71 1.82
1989 9 7.72 2.14
1990 9 6.43 1.98
1991 9 7.09 1.89
1992 9 3.27 2.96
1993 9 7.16 2.31
1994 9 5.99 2.19
1995 9 8.04 1.75
1996 9 5.14 2.73
1997 9 7.36 2.09
1998 9 6.12 1.76
1999 9 6.43 1.87
2000 9 5.62 1.89
2001 9 6.83 1.65
2002 9 6.89 1.99
2003 9 6.26 2.28
2004 9 5.10 2.64
2005 9 7.22 1.77
2006 9 6.91 1.82
2007 9 7.08 1.83
2008 9 6.27 2.17
2009 9 6.19 2.84
2010 9 7.04 2.48
2011 9 5.99 2.08
2012 9 5.88 2.09
2013 9 5.84 2.58
2014 9 6.68 2.30
2015 9 5.11 2.58
2016 9 7.07 2.44
2017 9 6.46 1.64
2018 9 7.83 1.61

#Mean daily temperatures across 38 year period

#histograms of percent habitat for each degree celcius - Chinook Presence habitat #histograms of percent habitat for each degree celcius - Chinook Spawning habitat

#histograms of percent habitat for each degree celcius - Chinook Rearing habitat

##Daily mean tempertures for each year (1980-2018) 

#Animate by Year using gganimate
#https://www.datanovia.com/en/blog/gganimate-how-to-create-plots-with-beautiful-animation-in-r/
#shadow fade with old years in background
theme_set(theme_bw())
ani <- ggplot(all_years, aes(x = day, y = mean_yr, color = as.factor(year))) +
  geom_smooth(se=FALSE, show.legend = FALSE) + 
  scale_size(range = c(2, 12)) +
  transition_states(year, transition_length = 1, state_length = 1) + shadow_mark(alpha=0.3, size=0.7) + 
  transition_time (year) + 
  labs(x = "Day of Year", y = "Daily mean Stream Temperature", title = "Year: {as.integer(frame_time)}")
  

animate(ani, duration=50, fps=1)
## `geom_smooth()` using method = 'loess' and formula 'y ~ x'

#try the "Let data gradually appear" with month time series
K_p2 <- preds %>% mutate(month=month(date), day2=(day(date))) %>% mutate(decade=case_when(year< 1990 ~ 1980, year >= 1990 & year < 2000 ~ 1990, year >=2000 & year < 2010 ~ 2000, year>2009 ~ 2010)) %>% filter(K_p == 1)  

all_years2 <- K_p2 %>% group_by(month, day2) %>% 
  summarize(mean_mth = mean(preds))

ani2 <- ggplot(all_years2, aes(x = day2, y = mean_mth, color=factor(month))) +
  geom_line() +
  labs(x = "Day of Month", y = "Stream Temperature", title = "Average Daily Temperatures 1980-2018") 

ani2 + transition_reveal(day2)

##Animate months by decade

all_years22 <- K_p2 %>% group_by(month, day2, decade) %>% 
  summarize(mean_mth_dec = mean(preds))

ggplot(all_years22, aes(x = day2, y = mean_mth_dec, color=factor(month))) +
  geom_line() +  facet_wrap(~decade) +
  labs(x = "Day of Month", y = "Stream Temperature", title = "Average Daily Temperatures by decade") 

ggsave("Anchor_chinook_plots/Average Daily Temps Animated.jpeg", plot=last_plot())
## Saving 4 x 4 in image
ani3 <- ggplot(all_years22, aes(x = day2, y = mean_mth_dec, color=factor(month))) +
  geom_line() + 
  labs(x = "Day of Month", y = "Stream Temperature", title = "Average Daily Temperatures by decade") 

ani3 + transition_reveal(day2) + facet_wrap(~decade)

##Summarize predictions by decades and plot

##Calculate and plot Temperature Anomolies!

#Filter for spawning time period - Chinook reach their spawning areas between July and September - DESCENDING LIMB!!!! #Filter for core rearing - June-August